This is a very mixed individual in terms of ancestry. As for the Malagasy people, we know both a lot and a little about them. They’re a hybrid population, more or less, of Austronesians with a very close connection to the to the Dayaks of southern Borneo. I have hypothesized that these Austronesians were part of a circum-Indian ocean trading network which was marginalized by the rise of Islam in the second half of the first millennium. Such an early date would explain why the Malagasy seem to have been only lightly touched by Indic cultural influences, let alone Islamic ones. There is also the African component to their ancestry, which is more prominent in the lowland populations to the west of the island of Madagascar. The Sakalava are a somewhat more African group (as opposed to the Merina of the eastern highlands, who are more Austronesian).

Below are some results from ADMIXTURE and PCA generated with EIGENSOFT. Most of the PCA plots were not too useful, because I didn’t fine-tune the populations ahead of time too much (this is a first pass), so I didn’t post them. The ADMIXTURE runs are those which seem highly informative to me. There were three data sets into which I merged the part-Malagasy individual:

#1 is plagued by a thin marker set. The Southeast Asian groups had ~56,000 markers, but the part-Malagasy individual only shared ~22,000 with them. Still, I made a go of it. I probably overcompensated in #2, as I used ~590,000 markers (the HGDP has a pretty good overlap with the 23andMe raw data). Finally, #3 had ~180,000 markers, which I feel to be very sufficient for this sort of exploratory endeavor.

Population

K1

K2

K3

K4

K5

K6

K7

K8

K9

K10

K11

K12

K13

Taiwan Aborigine

0%

0%

0%

2%

0%

0%

5%

23%

69%

0%

0%

0%

0%

Hmong

0%

0%

3%

78%

0%

0%

7%

4%

3%

2%

0%

0%

2%

Jinuo

0%

0%

73%

2%

0%

0%

9%

1%

1%

3%

1%

0%

9%

Wa

0%

0%

5%

4%

0%

0%

17%

2%

1%

7%

0%

0%

63%

Malagasy

31%

0%

2%

0%

6%

26%

0%

0%

0%

2%

31%

0%

3%

Alorese

0%

83%

0%

0%

1%

2%

0%

3%

2%

0%

0%

8%

0%

Javanese

0%

4%

1%

1%

0%

0%

1%

25%

8%

22%

1%

5%

32%

Lamaholot

0%

61%

0%

1%

1%

3%

1%

13%

7%

2%

0%

8%

2%

Mentawai

0%

0%

0%

0%

0%

0%

0%

98%

0%

1%

0%

0%

0%

West Javanese

0%

4%

1%

1%

0%

2%

0%

26%

9%

22%

1%

4%

31%

Toraja

0%

13%

0%

1%

1%

1%

3%

44%

21%

7%

0%

2%

5%

Indian

1%

1%

0%

0%

2%

59%

0%

0%

0%

1%

25%

1%

11%

Japanese

1%

1%

2%

3%

0%

1%

87%

1%

1%

1%

0%

0%

1%

Kensiu Negrito

0%

0%

0%

0%

0%

0%

1%

1%

1%

2%

0%

90%

4%

Utah, white

1%

0%

0%

0%

2%

20%

0%

0%

0%

0%

74%

0%

3%

Luhya

78%

0%

1%

0%

2%

18%

0%

0%

0%

0%

1%

0%

0%

Mamanwa

0%

1%

0%

0%

83%

0%

0%

9%

3%

0%

0%

2%

0%

West Mindanao

0%

6%

1%

4%

3%

3%

11%

36%

24%

5%

2%

1%

4%

West Luzon

0%

4%

1%

5%

2%

2%

16%

36%

24%

4%

1%

1%

4%

Karen

9%

1%

6%

6%

0%

0%

18%

2%

1%

8%

0%

1%

50%

Plang

1%

1%

8%

5%

0%

0%

12%

6%

2%

18%

1%

2%

43%

HTin

1%

0%

1%

1%

0%

0%

0%

2%

0%

84%

1%

0%

10%

Han Taiwan

0%

0%

6%

16%

0%

0%

45%

10%

13%

3%

0%

0%

7%

Population

K1

K2

K3

K4

K5

K6

K7

K8

K9

K10

Mbuti Pygmies

0%

100%

0%

0%

0%

0%

0%

0%

0%

0%

Biaka Pygmies

0%

9%

6%

0%

0%

0%

0%

59%

0%

25%

French

0%

0%

100%

0%

0%

0%

0%

0%

0%

0%

Papuan

1%

0%

0%

99%

0%

0%

0%

0%

0%

0%

Cambodians

75%

0%

0%

2%

10%

5%

8%

0%

1%

0%

Japanese

0%

0%

0%

0%

0%

0%

98%

0%

1%

0%

Han

28%

0%

0%

0%

0%

1%

70%

0%

1%

0%

Mandenka

0%

0%

0%

0%

0%

0%

0%

0%

0%

100%

Yakut

0%

0%

3%

0%

0%

0%

1%

0%

95%

0%

San

0%

0%

0%

0%

0%

0%

0%

100%

0%

0%

Bant S Africa

0%

4%

0%

0%

0%

0%

0%

23%

0%

73%

Tujia

34%

0%

0%

0%

0%

3%

63%

0%

0%

0%

Yizu

12%

1%

0%

1%

0%

9%

78%

0%

0%

0%

Miaozu

48%

0%

0%

0%

0%

1%

51%

0%

0%

0%

Hezhen

1%

0%

0%

0%

0%

1%

69%

0%

29%

0%

Xibo

4%

0%

2%

0%

1%

2%

73%

0%

18%

0%

Dai

88%

0%

0%

0%

0%

2%

10%

0%

0%

0%

Lahu

11%

0%

0%

0%

0%

82%

7%

0%

0%

0%

She

49%

0%

0%

0%

0%

0%

51%

0%

0%

0%

Naxi

4%

0%

0%

1%

0%

9%

85%

0%

1%

0%

Tu

8%

0%

4%

0%

3%

3%

74%

0%

7%

0%

Bantu Kenya

0%

5%

2%

0%

1%

0%

0%

7%

0%

84%

Malagasy

5%

1%

37%

0%

11%

3%

0%

4%

4%

36%

Indian

0%

0%

0%

0%

99%

0%

0%

0%

0%

0%

Population

K1

K2

K3

K4

K5

K6

K7

K8

K9

K10

Hadza

16%

0%

76%

1%

5%

1%

1%

1%

0%

0%

Yemen Jews

0%

0%

0%

84%

0%

0%

0%

0%

0%

15%

Ethiopian

19%

0%

4%

52%

25%

0%

1%

0%

0%

0%

Sandawe

6%

0%

1%

2%

90%

1%

0%

1%

0%

0%

Biaka Pygmies

0%

0%

0%

0%

0%

100%

0%

0%

0%

0%

Mbuti Pygmies

0%

0%

0%

0%

0%

0%

100%

0%

0%

0%

French

0%

0%

0%

20%

0%

0%

0%

0%

1%

80%

Cambodians

0%

100%

0%

0%

0%

0%

0%

0%

0%

0%

Mandenka

98%

0%

0%

0%

0%

1%

0%

0%

0%

0%

Yoruba

96%

0%

0%

0%

0%

4%

0%

0%

0%

0%

Bant S Africa

72%

0%

0%

0%

0%

9%

1%

17%

0%

0%

Bantu Kenya

77%

0%

1%

2%

12%

5%

2%

0%

0%

0%

Malagasy

32%

13%

0%

3%

5%

4%

1%

0%

7%

36%

Luhya

77%

0%

2%

1%

12%

5%

3%

0%

0%

0%

Indian

0%

1%

0%

0%

0%

0%

0%

0%

99%

0%

San

8%

2%

0%

1%

0%

1%

0%

79%

3%

6%

I don’t really trust the proportions for the Pan-Asian focused data set. But I figured I should report them. No idea why the Malagasy shows so much Yakut. Could be an artifact from the hybridization? As for the rest, it seems that the African ancestry of this individual isn’t too atypical for an East African Bantu.

(Republished from Discover/GNXP by permission of author or representative)

I would like to throw out the word that I am looking for a person with Malagasy ancestry for the African Ancestry Project. To my knowledge there are no thick marker autosomal analyses of the Malagasy people. After my recent exploration of Southeast Asian genetics I think even one individual would be highly informative.

As usual I would guarantee that these data are entirely private, and I do not share it with anyone. But in this case I would like to make an exception and stipulate that Joseph K. Pickrell, a graduate student at the University of Chicago, would also be very interested in access to a Malagasy genotype for the purposes of research. Since this is an undersampled population the marginal returns to a Malagasy genotype would be enormous for science, a public good rather than just a private gain.

Also, I am still looking for a Tutsi genotype so that I can ascertain the origin of this population.